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Author SHA1 Message Date
Serban Maerean
0598f70de2 patch petsc test cases for XL compiler (#8091) 
- After spack install, these test cases are built in a seperate step, outside of spack, but they need to patched after staging so users don't have to do it in a seperate step.

- The test cases are installed under `<petsc install directory>/share/petsc/examples` and can be built and executed by invoking `gmake -f gmakefile.test` in that directory.
 2018-05-14 23:53:05 -07:00
Robert Pavel
b956608631 Added Shim to Support hdf5+mpi in Spack Silo (#8130) 
* Added Shim to Support hdf5+mpi in Spack Silo

Added compatibility for hdf5+mpi to silo spackage to support spackages
with dependency chains that include silo and hf5+mpi

* Fixed fixable flake8 issue with silo spackage

Fixed missing whitespace around operator

* Setting MPI Variant to Default to True

As per guidance changing variant to default to MPI builds
 2018-05-14 20:29:03 -05:00
snehring
538d617d14 salmon: adding in version restriction for boost (#8129) 
1.67 does not work with this
 2018-05-14 18:48:28 -05:00
Cameron Smith
3a7fadd67e prenek missing X.h (#8121) 2018-05-14 18:19:46 -05:00
lingnanyuan
34a2d35e50 lordec: Create new package. (#8095) 
* lordec: Create new package.

* lordec: Add homepage, change to MakefilePackage.

* Modify dependency type.
 2018-05-14 16:56:49 -05:00
Eric
6cf1d25d14 r-fit-models: Create new package (#8122) 2018-05-14 16:50:54 -05:00
Eric
c5b1336b69 r-vipor: Create new package (#8128) 2018-05-14 16:38:59 -05:00
Brian Van Essen
281e22ed73 LBANN: add hydrogen as optional dependency (#8085) 
Add Hydrogen package for fork of Elemental library. Update LBANN
to use either Hydrogen or Elemental.
 2018-05-14 11:58:34 -07:00
Eric
e7a737621f r-shinydashboard: Create new package (#8116) 2018-05-14 13:00:18 -05:00
Eric
28982bd103 r-picante: Create new package (#8117) 
* r-picante: Create new package

* Remove dependency already included in RPackage base class
 2018-05-14 13:00:03 -05:00
Eric
f2cc7f769b r-squash: Create new package (#8118) 
* r-squash: Create new package

* Remove dependency already included in RPackage base class

* remove extra file
 2018-05-14 12:59:49 -05:00
Sajid Ali
a47ff73c6e Update py-llvmlite to reflect llvm@6 requirement for versions >0.23.0 (#8109) 
* 	new file:   package.py

* corrected using pep8online.com

* Update package.py

* correct typo

* as requested

* 	modified:   package.py

* Update package.py
 2018-05-14 11:26:01 -05:00
Levi Baber
b5d578a5e1 Aegean: new package (#8113) 
* aegean: new package

* genometools: set dependent env for aegean
 2018-05-14 11:10:19 -05:00
Christoph Junghans
1aef372fbf charliecloud: fix copyright (#8115) 2018-05-14 11:09:57 -05:00
Denis Davydov
42137d59ef dealii: another fix for quick tests only in 9.0 and thus hash (#8114) 2018-05-14 11:07:19 -05:00
健美猞猁
341132a87f A new pacakge: Kaiju. (#8111) 
* A new package: kaiju.

* Replace ftp:// with https://.
 2018-05-14 11:07:00 -05:00
Levi Baber
32662c4edb hisea: new package (#8112) 2018-05-14 09:46:54 -05:00
Sajid Ali
0dabe81a20 Add numexpr 3 (#8107) 
* 	new file:   package.py

* corrected using pep8online.com

* Update package.py

* correct typo

* as requested
 2018-05-14 09:46:14 -05:00
Denis Davydov
635f3e2969 dealii: update hash due to upstream changes (#8105) 2018-05-14 10:49:26 +02:00
healther
05cd983e10 add version 0.6.2 to yaml-cpp (#7931) 2018-05-14 10:44:27 +02:00
Sajid Ali
36b4c899fb Add cmake for newer version of libjpeg-turbo (#8102) 
* 	modified:   package.py

* add official build reference.

* Update package.py

* Update package.py

* Update package.py

* fixed with pep8online.com

* update make to make()

* change homepage
 2018-05-13 22:01:36 -05:00
Christoph Junghans
9f4c2a65a8 charliecloud: initial commit (#8106) 2018-05-13 22:00:18 -05:00
dorier
e758820ed7 boost: added the +numpy variant which enables building libboost_numpy (#8104) 
* added the +numpy variant which enables building the libboost_numpy libraries

* Update package.py

Added `type=('build', 'run')`
 2018-05-13 21:54:12 -05:00
Jon Rood
2d53043361 Create custom PATH that texlive requires in its module. (#8064) 
* Create custom PATH that texlive requires in its module.

* Updating texlive to 2018 distribution.

* Using platform instead of sys for easier portability across linux and osx.
 2018-05-12 18:40:36 -05:00
Yifan Zhu
8270344042 plink: new source version 1.9-beta5 (#8076) 
* plink: new source version 1.9-beta5

* plink: replace version 1.9 with 1.07
 2018-05-12 18:38:22 -05:00
George Hartzell
8dd5ac357c Add package for "bumpversion" (#8078) 
* Add package for "bumpversion"

bumpversion is a tool that automagically increments version numbers
for projects.  It can update files and do other magic along the way.

* Remove py- package prefix and use pypi.io URL

Renamed the package 'bumpversion'.

Fetch the package from pypi.io.

* Add version info for bumpverion@0.5.3
 2018-05-12 18:37:10 -05:00
Yifan Zhu
97f1b36c07 r-cdcfluview: new package (#8089) 
* r-cdcfluview: new package

* updated package.py
 2018-05-12 18:28:18 -05:00
Massimiliano Culpo
867bd9b48c
nfft: added version 3.4.1 Moved package to github (#8099) 2018-05-12 17:25:28 +02:00
Massimiliano Culpo
36ee0cbf88
netcdf: added version 4.6.1 (#8098) 2018-05-12 17:24:59 +02:00
Yifan Zhu
262de64792 shoremap: new package (#7343) 2018-05-12 08:22:45 +02:00
Denis Davydov
e271f14493 dealii: add 9.0.0 (#8096) 2018-05-11 21:59:25 -05:00
Howard Pritchard
efbc230742 pmix: add 1.2.5 and 2.0.3 bug fix releases (#8097) 
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
 2018-05-11 21:58:29 -05:00
Levi Baber
35e1af9acc masurca: new version (#8094) 
* masurca: new version

* masurca: reorder versions
 2018-05-11 14:43:21 -05:00
scheibelp
79669ac647
llvm: replace @when with internal check in @run_before (#8092) 
Fixes #8088

#7012 added a @when condition for a @run_before check to constrain
that check to only run on Darwin. @when is intended to be used to
choose one of several different implementations of a given function
and cannot be used to conditionally deactivate a check altogether.

This replaces the external decorator with a check that executes at
the beginning of the function.
 2018-05-11 12:32:26 -07:00
Mayeul d'Avezac
5bc970f9b6 adds new version to swiftsim (#8093) 2018-05-11 10:32:30 -05:00
Denis Davydov
28bebe13a8 dealii: disable tpetra when +cuda; check for '' in cuda_arch (#7958) 
* dealii: disable tpetra when +cuda; check for '' in cuda_arch

* trilinos: fix Kokkos CUDA

* Revert "trilinos: fix Kokkos CUDA"

This reverts commit 6aae894bc7d49c9e736c06f65b81b8c219443920.

* update according to @aprokop comments

* minor

* fix flake8
 2018-05-11 08:50:35 -05:00
Denis Davydov
206e61bafd gmsh: add netgen and tetgen (#8060) 
* gmsh: add netgen and tetgen
dealii: require gmsh+netgen+tetgen
netgen: use http instead of https

* dealii: add oce requirement to gmsh
 2018-05-11 14:22:12 +02:00
Yifan Zhu
55473dd321 r-mmwrweek: new pacakge (#8086) 2018-05-10 17:32:58 -05:00
David Wootton
9c4522ecbd petsc: specify number of processors used for test case (#8015) 
For Spectrum MPI, if -np is omitted, the default behavior is to
assign one process per process slot, where the default process slot
allocation is one per core. On systems with many cores, the number
of processes can exceed the size of the grid specified when the
testcase is run and the test case fails. This specifies a small
number of processes when running the test case to prevent failure.
 2018-05-10 10:49:18 -07:00
healther
f4a46f4fc3 wireshark: stop cmake from picking up /usr paths (#8053) 
* stop cmake from picking up /usr paths if spack has corresponding packages

Change-Id: I7217122562697c7a642cded2b4bfb606d2e35ffb

* add libpcap dependency

Change-Id: If0d5c2c94b2c2d1cbb9b19e31e44f870b71ba88b

* make cmake actually pick up pcap

Change-Id: I67b87fd9282c26f5ff4e0a5aedd8bbbae39a5960

* add libtool build dependency

Change-Id: I5c6d14dca7ccbe457318903dd170bb19d004e952

* use .libs for pcap

Change-Id: Ibe78f8765524385f9da4a8f9963f2c61632cc9f7

* explicitly add bison build dependency

Change-Id: I47112778abdf4c0de81789685a7eca4dddb20f77

* add lua explicitly

Change-Id: I8e306e1e4cfa0e16138f3a5109ddcfe912120946

* fix libs usage

Change-Id: I8c1e03f10df69e3ef74326a13cacaf0e5498e6aa

* add minimal version requirement

Change-Id: I4dd181389f9a63067df541b982bc0727f974d4ce
 2018-05-10 06:58:43 -05:00
David Gardner
1f8fc574d9 Add new Sundials versions (#8075) 
* Add new Sundials versions, update minimum cmake version required

* specify which versions require a newer cmake

* revise cmake dependency

* remove develop, add 4.0.0-dev version
 2018-05-09 20:53:25 -05:00
mcneish1
cadf9242ba Add 3.5.2; Add optional cpp implementation enable for py-protobuf (#8069) 
* Add 3.5.2; Add optional cpp implementation enable for py-protobuf

* Make flake8 happy

* Give all required install_args
 2018-05-09 20:52:39 -05:00
Eric
ef731cc511 perl-extutils-pkgconfig: Add pkg-config dependency (#8045) 
* perl-extutils-pkgconfig: Add pkg-config dependency

* perl-extutils-pkgconfig: fix build dependency

* perl-extutils-pkgconfig: fix build dependency
 2018-05-09 13:10:36 -05:00
Geoffrey Oxberry
7dfc0278e7 llvm+lldb plaform=darwin: check for lldb_codesign certificate (#7012) 
* llvm+lldb plaform=darwin: check for lldb_codesign

Building LLVM with LLDB requires that the "lldb_codesign" code
certificate be created (see
https://llvm.org/svn/llvm-project/lldb/trunk/docs/code-signing.txt for
details). This commit checks for this certificate on Darwin if LLDB is
to be built, and returns an informative error message if this
certificate is unavailable.
 2018-05-09 15:04:06 +02:00
mcneish1
4277b42ddc Add gdb@8.1; add optional lzma dependency for debug information support (#8068) 2018-05-08 21:08:39 -05:00
Brian Van Essen
a9e47b763e opencv updates for lbann (#6502) 
Add variants to control building of many 3rd-party modules in opencv.
They are enabled by default, which matches the defaults chosen by
opencv when these options are not set explicitly. This also updates
the lbann opencv dependency to disable most of these new variants by
default in order to build faster.
 2018-05-08 17:55:12 -07:00
Massimiliano Culpo
b4859e10e2 Packages can tune the list of files to be archived at the end of install (#7760) 
Fixes #2781

This PR introduces a new attribute for packages called
`archive_files`, which designates files that should be saved from
a package build (e.g. the config.log generated during autotools
builds).

The attribute contains a list of glob expressions; Any file that
matches will be archived in the `<prefix>/.spack/archived-files`
directory. Errors that occur when archiving files are collected and
reported in a file named `<prefix>/.spack/archived-files/errors.txt`.

`AutotoolsPackage` and `CMakePackage` provide a sensible default
override for this attribute.
 2018-05-08 17:40:53 -07:00
peetsv
50a95c57c7 Py cnvkit: updating dependencies (#8057) 
* py-pyfaidx: adding new package

* updating the url

* identifying dependencies
 2018-05-08 17:54:15 -05:00
Gregory Lee
c12dd61358 intltool requires patching for newer perl versions (#8061) 2018-05-08 17:53:50 -05:00
Gregory Lee
804a7991e0 added stat version 4.0.0 (#8062) 2018-05-08 17:52:38 -05:00
Gregory Lee
16adf144c2 added shared-mime-info version 1.9 (#8063) 2018-05-08 17:52:02 -05:00
Andrew Gaspar
29b11f624f Updates to Google Benchmark package: (#8056) 
- Adds v1.3.0 and v1.4.0
- List explicit CMake version dependency (from Benchmark CMake files)
- Disable the building of tests. Starting in v1.4.0 this introduced a dependency on GoogleTest

Tested by building all versions on macOS High Sierra
 2018-05-08 13:04:19 -05:00
Ce Qin
bb5ef39ad2 Fix superlu-dist with PETSc 3.9.0 (#8048) 2018-05-08 12:44:38 -05:00
Axel Huebl
7ff034a55d pybind11: v2.2.3 (#8051) 
* pybind11: 2.2.3

new release for pybind11, v.2.2.3:

https://github.com/pybind/pybind11/blob/v2.2.3/docs/changelog.rst#v223-april-29-2018

* pybind11: compiler support

mark older versions as conflicts
 2018-05-08 12:43:38 -05:00
Geoffrey Oxberry
ca9ce8048c googletest: add variant to enable/disable threads (#8052) 
Add Google Test variant to enable/disable building with threads.
 2018-05-08 12:42:57 -05:00
Levi Baber
0ac777b88e openmpi: new version (#8055) 2018-05-08 12:35:44 -05:00
Yifan Zhu
3a5f68c078 r-genie3: new package (#8044) 2018-05-07 17:23:45 -05:00
Eric
d6c6a7016f manta: Create new package (#8043) 
* manta: Create new package

* manta: Create new package

* manta: fix dependency types
 2018-05-07 17:22:43 -05:00
Eric
fa93df49bd py-pysqlite: Create new package (#8042) 2018-05-07 13:42:24 -05:00
Denis Davydov
3a88227c83 perl: add 5.26.2 (#7984) 
* perl: add 5.26.2

* perl: add 5.22.4

* move Misc releases to EOL
 2018-05-07 13:40:32 -05:00
Christoph Junghans
b5c6bbb2a2
pkgconf: use alpine linux mirror to avoid ssl error (#8039) 2018-05-07 10:46:58 -06:00
anne-glerum
9557a6881f Add patch (#8034) 2018-05-07 09:51:27 -05:00
Andrey Prokopenko
231664e22c trilinos: minor cleanup (#7987) 2018-05-07 06:45:49 -05:00
Eric
df575382ba py-dlcpar: Add package description (#8032) 2018-05-07 06:44:16 -05:00
Stephen McDowell
506f8e9f3e add opencv 3.4.1 (#8031) 2018-05-06 21:40:27 -05:00
Eric
0dddb98869 metabat: Create new package (#7991) 
* metabat: Create new package

* fix Perl script shebangs and BOOST_ROOT environment

* add perl script fix function

* add perl dependency and fix positional argument for Python 2.6
 2018-05-06 10:56:03 -05:00
healther
17ce5fd912 Add package wireshark and dependencies (#8024) 
* add wireshark

Change-Id: I1ef674ff286db2e06baaf9fca65982d1145cfa79

* fix qt4 build

Change-Id: Ieb9989b9fec1a0e02388197f971ee66b591d45c5

* remove commented lines

Change-Id: Ia67bfaf1beba06dd710cee56aec06bc36b293d34

* flake8 fix

Change-Id: Ica1b2cce2be2faca82a4177c3cdc3a0bb005c031

* remove clutter

Change-Id: I6061fe56a88f8c7b7e03fdce5e3eae04036ad2d8

* fix dependencies

Change-Id: I8160c70c9333c9f5e82ed5fc73633455df568972

* use dot syntax instead of join_path

Change-Id: Id1f737299b603fa4093b58571d46a64b0dd84895
 2018-05-06 09:32:06 -05:00
Adam J. Stewart
b83be5f2d4
macOS-specific patch no longer applies to GCC 8 (#8029) 2018-05-06 09:28:33 -05:00
Elizabeth Fischer
f3c9b98bbd py-udunits: New package (#7998) 
* py-udunits: update

* Use standard py-netcdf4

* Remove unnecssary import?

* Suggested simplifications

* flake8
 2018-05-05 17:33:44 -05:00
健美猫
e499a4d071 A new library: libshm. (#8028) 2018-05-05 17:16:48 -05:00
健美猫
dfe0752807 Bump pysam to 0.14.1. (#7988) 
* py-pysam requires curl.

* py-pysam conflicts with htslib@1.7.

* Bump py-pysam versions.

* Add more dependencies.
 2018-05-04 22:11:26 -05:00
sknigh
4fe6d9acee Added GCC 8.1.0 (#8026) 
Built once on Centos 7 w/ external GCC 4.8.5 compiler
 2018-05-04 18:52:03 -05:00
Jungwon Kim
cd80c7cf18 a new package: papyrus. (#8023) 
* a new package: papyrus.

* removed the empty cmake_args

* changed md5 checksum for v1.0.0

* make a long line short

* one long line url
 2018-05-04 18:51:37 -05:00
健美猫
c53541e448 Bump samtools, hstlib and bcftools to version 1.8. (#8020) 
* Bump samtools and hstlib to version 1.8.

* rm .bak.

* Bump bcftools to 1.8.

* bcftools@1.8 depends on libzip.
 2018-05-04 16:27:54 -05:00
Elizabeth Fischer
490cde87dd py-more-itertools: new package (#8004) 
* py-more-itertools: new package

* code review
 2018-05-04 16:27:14 -05:00
健美猫
51c2dbb707 Hic-Pro: fix a typo and replace hard-coded version. (#8022) 
* Fix a typo and replace hard-coded version.

* version -> self.version.
 2018-05-04 10:56:04 -05:00
Massimiliano Culpo
0570b075d4
openmpi: don't build static libraries if slurm is activated (#8021) 
According to this comment:

    https://github.com/open-mpi/ompi/issues/4338#issuecomment-383982008

on an OpenMPI issue, using `--enable-static` silently disable slurm
support.
 2018-05-04 16:27:54 +02:00
Elizabeth Fischer
593ad23a9f gdal: update (#8008) 
* gdal: update

* Remove unneeded depends(python)
 2018-05-03 22:55:31 -05:00
健美猫
0812fd1635 Bump r-rcpp versions. (#8016) 2018-05-03 22:54:45 -05:00
Elizabeth Fischer
ea4829880f pism: new package (#8010) 
* pism: new package

* Implement code review

* Remove pointless docstring5

* Fixed missing trailing quote
 2018-05-03 22:54:00 -05:00
Elizabeth Fischer
d52eb8b34d py-numpy: update (#8003) 
* py-numpy: update

* Better constrain when can / cannot parallel build.

* Update SciPy parallel logic to be specific to Python 3.5+, same as in Numpy.
 2018-05-03 22:53:41 -05:00
Elizabeth Fischer
60c1e41e4c py-bsddb3: update (#8006) 
* py-bsddb3: update

* Change py-setuptools to build dependency
 2018-05-03 19:20:14 -05:00
Elizabeth Fischer
ffcf3ef2c8 pfunit: update (#7994) 2018-05-03 17:02:20 -05:00
Elizabeth Fischer
28adaa4e55 Everytrace: update (#7995) 2018-05-03 17:00:21 -05:00
Elizabeth Fischer
7542fbfefd py-yamlreader: new package (#7997) 2018-05-03 16:58:40 -05:00
Elizabeth Fischer
5656529974 gmp: update (#7999) 2018-05-03 16:53:19 -05:00
Elizabeth Fischer
bf896c5a43 py-scipy: update (#8000) 2018-05-03 16:52:46 -05:00
Elizabeth Fischer
e93c880a79 py-pyside: update (#8002) 2018-05-03 16:50:55 -05:00
Elizabeth Fischer
ebca867496 py-cython: update (#8005) 2018-05-03 16:46:15 -05:00
Eric
2aea56da07 genomefinisher: Create new package (#7989) 2018-05-03 13:11:00 -05:00
Eric
a128fa88c5 py-crispresso: Create new package (#7990) 
* py-crispresso: Create new package

* py-crispresso: Create new package
 2018-05-03 13:09:59 -05:00
Kelly (KT) Thompson
7846dfa817 New Package: ruby-svn2git (#7979) 
* New Package: svn2git

https://github.com/nirvdrum/svn2git

svn2git is a tiny utility for migrating projects from Subversion to Git while
keeping the trunk, branches and tags where they should be. It uses git-svn to
clone an svn repository and does some clean-up to make sure branches and tags
are imported in a meaningful way, and that the code checked into master ends up
being what's currently in your svn trunk rather than whichever svn branch your
last commit was in.

* Actually requires +perl variant of subversion.

* fix style issue.
 2018-05-03 10:12:57 -05:00
健美猫
c8157e31e1 A new package: nanopb. (#7981) 
* A new package: nanopb.

* flake8.

* Remove py-pytorch.
 2018-05-03 10:12:37 -05:00
健美猫
78d8bd7d40 Bump pgi to 18.4. (#7980) 
* Bump pgi to 18.4.

* Remove the empty line.

* Update.
 2018-05-03 10:12:17 -05:00
健美猫
05f51c46dd Bump gatk version to 4.0.4.0. (#7985) 
* Bump gatk version to 4.0.4.0.

* Update.

* Fixed.

* Fixed.
 2018-05-03 10:08:48 -05:00
健美猫
fb9898230e A new package: py-openslide-python. (#7907) 
* A new package: py-openslide-python.

* Update.

* Remove py-pytorch package.

* Remove nektar package.

* Remove install_time_test_callbacks
 2018-05-03 08:37:52 -05:00
Michael Kuhn
937ab7d5cc go: Update to 1.10.2 (#7982) 2018-05-03 12:14:52 +02:00
Elizabeth Fischer
cbd77e3a8d make symlinking python3->python optional (#7960) 
* Make symlinking python3->python optional
* Added reference to PEP 394
 2018-05-02 12:26:30 -07:00
Adam Moody
7909e15d83 mvapich2: add 2.3rc2 (#7976) 2018-05-02 14:23:32 -05:00
Elizabeth Fischer
f054fa2f43 sphinx: Updated to v1.7.4 (#7977) 
* sphinx: Updated to v1.7.4

* Update package.py
 2018-05-02 14:23:02 -05:00